Yes, this is due to an improvement. Set the pbcatom (as the error message tries to say) for the pull groups mentioned. The options are described in the mdp section of the manual.
Berk ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Sunday, February 24, 2019 6:55 AM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Pull code errors Hi, There have been some improvements to the pull code, but I don't know offhand whether they apply here. Do consult the 2019 release notes for clues. Mark On Sat., 23 Feb. 2019, 06:11 Ayesha Fatima, <ayeshafatima...@gmail.com> wrote: > Dear All, > I am using Gromax 2019 and running an umbrella sampling for two proteins. > It is a simple pulling simulation. It is giving me the following error > > > ERROR 1 [file md_pull.mdp]: > When the maximum distance from a pull group reference atom to other atoms > in the group is larger than 0.5 times half the box size a centrally > placed atom should be chosen as pbcatom. Pull group 1 is larger than that > and does not have a specific atom selected as reference atom. > > > ERROR 2 [file md_pull.mdp]: > When the maximum distance from a pull group reference atom to other atoms > in the group is larger than 0.5 times half the box size a centrally > placed atom should be chosen as pbcatom. Pull group 2 is larger than that > and does not have a specific atom selected as reference atom. > > Pull group natoms pbc atom distance at start reference at t=0 > 1 9157 4579 > 2 589 5113 0.300 nm 0.300 nm > Estimate for the relative computational load of the PME mesh part: 0.14 > > > ---------------------------------------------------------------------------------- > Is there anything to be added in the pull code? > > Thank you > Regards > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
